LRC: Identify DCGs (Differential Coexpressed genes) based on 'Log...

In DCGL: Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data

Description

A method to pick out DCGs from microarray data based on 'Log Ratio of Connections' (LRC) (Reverter et al. 2006).

Usage

LRC(exprs.1, exprs.2, link.method = c("qth", "rth", "percent")[1], cutoff)

Arguments

exprs.1	a data frame or matrix for condition A, with rows as variables (genes) and columns as samples.
exprs.2	a data frame or matrix for condition B, with rows as variables (genes) and columns as samples.
link.method	a character string indicating link filtering method, default is 'qth'.
cutoff	cutoff used for link filtration, can be rth, qth, or percent depending on link.method. must be within [0,1].

Details

'Log Ratio of Connections' (LRC) calculates the logarithm of the ratio of the connectivities of a gene between two conditions (Reverter, et al., 2006). A connectivity of zero is changed to one.

Value

LRC	the log Ratio Connections of genes. This measure can be used to rank gene in terms of differential coexpression.

Author(s)

Bao-Hong Liu, Hui Yu, Jing Yang

References

Reverter, A., Ingham, A., Lehnert, S.A., Tan, S.H., Wang, Y., Ratnakumar, A. and Dalrymple, B.P. (2006) Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer, Bioinformatics, 22, 2396-2404.

Examples

data(exprs)
LRC(exprs[1:100,1:16],exprs[1:100,17:63],link.method = 'qth', cutoff=0.25)

Example output

      AACS      FSTL1      ELMO2    CREB3L1      RPS11      PNMA1       MMP2 
0.66900678 0.70679534 0.41345217 0.82118588 0.98741087 1.10720997 0.40748533 
    SAMD4A    SMARCD3      A4GNT     PKNOX2      RALYL       ZHX3      ERCC5 
1.28630674 0.18563658 0.18563658 0.85867085 0.66005194 0.90308999 0.63920180 
     GPR98      RXFP3      APBB2      BBOX1    PRO0478        XDH       EDN1 
0.60205999 0.75587486 0.93785209 1.59106461 0.10473535 0.49884050 0.73468556 
     MTERF        AEN       CLK4      KCNG1      CXCR4      DECR1      SALL1 
0.88930170 0.23888209 0.39445168 0.34748740 0.77815125 0.76591679 0.35024802 
     PTPRR      CADM4      IRAK1      CFHR5     TMSB10      CXCL3      LMAN1 
0.71321044 0.17168214 1.23044892 1.05435766 1.76342799 0.62838893 0.43230891 
      CHD8      SUMO1      GP1BA     OR7A10       DDB1    CHRNA10      STYK1 
0.23044892 0.89526465 0.66900678 0.77815125 0.47712125 0.20994953 0.58357659 
     MYO9B       CCNI       MMP7      EP300     CRNKL1    C9orf45       XAB2 
0.61395921 0.65321251 0.64626365 0.05799195 0.44834951 0.92427929 0.21912589 
      RTN1       HIC2      TBX10      CENPQ        UTY      OR2W1      KCNA6 
0.97772361 0.26884531 0.32658410 0.59207577 0.92941893 0.61729996 0.47078108 
    ATP5G2       ZEB1        ERG       FAT4       PARN       SOD2      CYTH1 
0.53360261 0.51490982 0.16481025 0.39064077 0.19382003 0.32221929 0.68921017 
    ADAM5P       CHD9      STK16      PDE1C     SEMA4D     AGPAT1       TOB2 
0.88223985 0.42596873 0.32735893 0.39794001 0.23888209 0.00000000 0.07255067 
     BANK1     MAP3K3        MAX       GRM2     OSBPL8      PROSC      NR4A2 
0.82930377 0.19629465 0.33579210 1.75587486 0.64998354 0.75012253 0.50514998 
      RICS        PIR       PPCS       IPO9      LONP1        EVC     CXCL13 
1.01424044 1.26717173 1.68124124 0.07058107 0.57723641 0.83614320 0.32735893 
     FFAR3      SCYL3   KIAA1199      SORL1      NAT10       CHD1       SYN3 
0.27470106 0.41642341 0.91381385 0.55428721 0.25712451 0.22724378 0.66005194 
      DMC1    SLC22A2   SERPINF1   C20orf27     OR7A17    RPS6KA5       HMX1 
0.83108733 0.57573105 0.50514998 0.30776338 0.13683796 0.13188760 0.34406463 
    DHRS11        LHB 
0.32585358 0.23044892 

DCGL documentation built on May 1, 2019, 8:38 p.m.